Unfortunately, that's classic with stainless (and blued) guns wearing Hogue synthetic grips. Moisture and dirt get under the grip and boom, that's all she wrote.
People often think that Stainless steel is rust proof, it is not, it is just corrosion resistant.
I have a 1006 pistol and a 629-4 that experienced that issue, and after learning my lesson, I now keep a coat wax on the frame under the grips of all of my guns.
Yes, rubber grips are notorious for trapping moisture and allowing rust. Stainless steel isn’t rust proof, it’s rust Resistant.
I typically remove the grips when I do a deep cleaning (once or twice a year). It ‘s a good idea to wax the frame under the grips while you have them off.
I don’t like to bash Hogue because I believe they are a good company and they are good people but the main reason I don’t like their Monogrips is that clip gets rusted pretty easily. It’s probably cost prohibitive but it would be nice if they could make a stainless clip.
After cleaning it up some more, I would use some Corrosion X oil on the rusted areas. I usually let the Kroil sit and brush a couple times a day with a bronze brush for a period of at least 3 days to get rid of the rust. Wear gloves when using Kroil because it will penetrate into you if you don’t and it is nasty stuff.
Most people do not know there are two common grades of stainless steel. 300-grade is truly stainless and usually will not corrode but 400-grade, the type guns are made from, contains some carbon as a hardener and will corrode. But as you learned, while it can be a shocking sight, it cleans up fairly easily.
And, combined with some 3-in-1 oil, they worked perfectly for cleaning rust off my recently acquired M30 while not damaging the bluing.
The other thing you can do is coat the area under the grip with Renaissance Wax or Rust Inhibition Grease (RIG). Either should slow that down quite a bit.
Update: I just didn't feel right with this rust not being disclosed. The FFL offered a refund and I accepted. I did purchase a replacement this morning: 629-4 Ported. They removed the grips while on the phone and said no rust or pitting. The finish is not quite as good but expect it is 90%. The price was a lot less too! Thanks for everyone's advice and suggestions.
Don't worry, that's just surface rust. It'll clean up with little effort. When I bought my 629-3, I discovered similar rust beneath the Hogue grips and other places where the sun don't shine. Have at it with some penetrating oil, a brash brush, or scotch pad, or a rag and some elbow grease... then oil it very lightly or wax it as others have suggested.
A coating of wax under the stocks to repel moisture is a great idea, as noted above. If the gun gets wet, remove the grips/stock panels, dry and re-wax. Also, for future rust removal be sure to use bronze wool or something else besides steel wool; the latter will embed small particles in the gun that will make it more likely to rust. Enjoy!